Comparison of expression in Arabidopsis mutant tdt-1 and wild type
ABSTRACT: The object of this study was to explore whether the loss of mRNA decapping in the Arabidopsis mutant tdt-1 resulted in global dfferences of RNA profiles, as compared to wild type. Keywords: Genetic modification affect on gene expression Overall design: In this experiment we compared expression in tdt-1 and wild type 3 day whole seedlings. We performed three biological replicates, in which one experiment was dye-swapped.
INSTRUMENT(S): Agilent-012600 Arabidopsis 3 Oligo Microarray (4142A (Feature Number version)
Project description:The object of this study was to explore whether the loss of mRNA decapping in the Arabidopsis mutant tdt-1 resulted in global dfferences of RNA profiles, as compared to wild type. Experiment Overall Design: In this experiment we compared expression in tdt-1 and wild type 3 day whole seedlings. We performed three biological replicates, in which one experiment was dye-swapped.
Project description:We used microarrays to assess gene expression differences in the hippocampus between FoxO6 mutant and wild-type siblings before (basal) or after novel object learning. The cohort of basal mice were housed individually for at least 3 days prior to tissue harvesting. The mice used to collect hippocampal samples after the object learning task were handled daily in the procedure room, prior to the object learning task. 24 hours before the object learning task, each mouse was individually habituated to the empty novel object arena for 10 min. On the days of the novel object learning task and the empty arena habituation, the mice were transferred to the procedure room and acclimatized for 60 min. For the novel object learning task, the mice were allowed to explore two identical and novel objects for 10 min in a 70 x 70 x 70 cm black plastic arena with a white PVC vinyl material on the base. After the object exploration, mice were transferred to an empty cage, and were euthanized after 60 min. The brains were dissected and incubated in ice-cold RNAlater (Ambion) for 24 hours at 4ºC. The brains were then rapidly frozen in O.C.T. Tissue-Tek (Sakura) at -80ºC. Coronal brain sections (300 µm) were made using a microtome (Microm), the hippocampus was finely dissected and collected into ‘RNA lysis buffer’ (Ambion), and homogenized for 30 sec using a rotar-stat homogenizer. Total RNA was extracted using the RNAqueous column (Ambion) following the manufacturer’s protocol.
Project description:To assess the role of the decapping activator Scd6 in mRNA decay, we used RNA-Seq to analyze the expression profile of yeast cells harboring a deletion of the SCD6 gene. Consistent with our recent model for decapping regulation, we found that Scd6 targets a small number of specific mRNAs in yeast cells. Interestingly, degradation of Scd6-targeted transcripts also requires the functions of the decapping activators Pat1, Lsm1, and Dhh1, suggesting that Scd6 functions together with Pat1, Lsm1, and Dhh1 in promoting mRNA decapping. Overall design: Genome-wide expression profiles of the wild-type and scd6∆ strains were generated by RNA-Seq, in triplicate, using Illumina HiSeq4000. Transcripts differentially expressed in the scd6∆ strain were identified by comparing to the wild-type strain.
Project description:The goal of this experiment is to identify transcripts regulated by Edc3p, an activator of mRNA decapping. Experiment Overall Design: Five independent expression profiling experiments were carried out for isogenic wild-type (HFY114) and edc3Δ (CFY25) strains using Affymetrix Yeast Genome S98 Arrays.
Project description:Transcriptional profiling of Deinococcus radiodurans comparing control untreated wild type cells with wild type cells treated with 0.3M NaCl or 2M NaCl Two-condition experiment, wild type vs. 0.3 M NaCl. Biological replicates: 4 replicates (Two replicates per array, N=8), dye-swapped, independently grown and harvested. Two-condition experiment, wild type vs. 2 M NaCl. Biological replicates: 4 replicates (Two replicates per array, N=8), dye-swapped, independently grown and harvested.
Project description:To assess the roles of the Dcp2 C-terminal domain and the decapping activators Pat1, Lsm1, and Dhh1 in mRNA decapping, we used RNA-Seq to analyze the expression profiles of yeast cells harboring a truncation of the Dcp2 C-terminal domain, mutations that render Dcp2 catalytically inactive, or deletions of the PAT1, LSM1, and DHH1 genes. Consistent with our recent model for decapping regulation, we found that: i) the Dcp2 C-terminal domain is an effector of both negative and positive regulation and that loss of these control functions causes significant deregulation of mRNA decapping; ii) rather than being global activators of decapping, Pat1, Lsm1, and Dhh1 directly target specific subsets of yeast mRNAs and loss of the functions of each of these factors has substantial indirect consequences for genome-wide mRNA expression; and iii) transcripts targeted by Pat1, Lsm1, and Dhh1 exhibit only partial overlap and, as expected, are targeted to decapping-dependent decay. Overall design: Genome-wide expression profiles of the wild-type strain and each of the mutant strains were generated by RNA-Seq, in triplicate, using Illumina HiSeq4000. The transcripts differentially expressed in different mutant cells were identified by comparisons to the transcripts expressed in wild-type cells.
Project description:Global analysis of gene expression in 10 day old brm-101 and syd-2 mutant seedlings compared to wild type Landsberg erecta seedlings. Experiment Overall Design: 3 genotypes (2 mutant, 1 wild type), 2 replicates each